---
_id: '7770'
abstract:
- lang: eng
text: Packings of frictionless athermal particles that interact only when they overlap
experience a jamming transition as a function of packing density. Such packings
provide the foundation for the theory of jamming. This theory rests on the observation
that, despite the multitude of disordered configurations, the mechanical response
to linear order depends only on the distance to the transition. We investigate
the validity and utility of such measurements that invoke the harmonic approximation
and show that, despite particles coming in and out of contact, there is a well-defined
linear regime in the thermodynamic limit.
article_number: '022201'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in
jammed particulate packings. Physical Review E. 2014;90(2). doi:10.1103/physreve.90.022201
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Contact nonlinearities
and linear response in jammed particulate packings. Physical Review E.
American Physical Society. https://doi.org/10.1103/physreve.90.022201
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities
and Linear Response in Jammed Particulate Packings.” Physical Review E.
American Physical Society, 2014. https://doi.org/10.1103/physreve.90.022201.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear
response in jammed particulate packings,” Physical Review E, vol. 90, no.
2. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response
in jammed particulate packings. Physical Review E. 90(2), 022201.
mla: Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in
Jammed Particulate Packings.” Physical Review E, vol. 90, no. 2, 022201,
American Physical Society, 2014, doi:10.1103/physreve.90.022201.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).
date_created: 2020-04-30T11:42:24Z
date_published: 2014-08-04T00:00:00Z
date_updated: 2021-01-12T08:15:25Z
day: '04'
doi: 10.1103/physreve.90.022201
extern: '1'
fulldoi: https://doi.org/10.1103/physreve.90.022201
intvolume: ' 90'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Contact nonlinearities and linear response in jammed particulate packings
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 90
year: '2014'
...
---
_id: '7771'
abstract:
- lang: eng
text: 'In their Letter, Schreck, Bertrand, O''Hern and Shattuck [Phys. Rev. Lett.
107, 078301 (2011)] study nonlinearities in jammed particulate systems that arise
when contacts are altered. They conclude that there is "no harmonic regime in
the large system limit for all compressions" and "at jamming onset for any system
size." Their argument rests on the claim that for finite-range repulsive potentials,
of the form used in studies of jamming, the breaking or forming of a single contact
is sufficient to destroy the linear regime. We dispute these conclusions and argue
that linear response is both justified and essential for understanding the nature
of the jammed solid. '
article_number: '049801 '
article_processing_charge: No
article_type: letter_note
arxiv: 1
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Comment on “Repulsive contact interactions make
jammed particulate systems inherently nonharmonic.” Physical Review Letters.
2014;112(4). doi:10.1103/physrevlett.112.049801
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Comment on “Repulsive
contact interactions make jammed particulate systems inherently nonharmonic.”
Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.112.049801
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Comment on ‘Repulsive
Contact Interactions Make Jammed Particulate Systems Inherently Nonharmonic.’”
Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/physrevlett.112.049801.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Comment on ‘Repulsive contact
interactions make jammed particulate systems inherently nonharmonic,’” Physical
Review Letters, vol. 112, no. 4. American Physical Society, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Comment on “Repulsive contact interactions
make jammed particulate systems inherently nonharmonic”. Physical Review Letters.
112(4), 049801.
mla: Goodrich, Carl Peter, et al. “Comment on ‘Repulsive Contact Interactions Make
Jammed Particulate Systems Inherently Nonharmonic.’” Physical Review Letters,
vol. 112, no. 4, 049801, American Physical Society, 2014, doi:10.1103/physrevlett.112.049801.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review Letters 112 (2014).
date_created: 2020-04-30T11:42:39Z
date_published: 2014-04-20T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '20'
doi: 10.1103/physrevlett.112.049801
extern: '1'
external_id:
arxiv:
- '1306.1285'
fulldoi: https://doi.org/10.1103/physrevlett.112.049801
intvolume: ' 112'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1306.1285
month: '04'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
issn:
- 0031-9007
- 1079-7114
publication_status: published
publisher: American Physical Society
status: public
title: Comment on “Repulsive contact interactions make jammed particulate systems
inherently nonharmonic”
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2014'
...
---
_id: '7772'
abstract:
- lang: eng
text: Particle tracking and displacement covariance matrix techniques are employed
to investigate the phonon dispersion relations of two-dimensional colloidal glasses
composed of soft, thermoresponsive microgel particles whose temperature-sensitive
size permits in situ variation of particle packing fraction. Bulk, B, and shear,
G, moduli of the colloidal glasses are extracted from the dispersion relations
as a function of packing fraction, and variation of the ratio G/B with packing
fraction is found to agree quantitatively with predictions for jammed packings
of frictional soft particles. In addition, G and B individually agree with numerical
predictions for frictional particles. This remarkable level of agreement enabled
us to extract an energy scale for the interparticle interaction from the individual
elastic constants and to derive an approximate estimate for the interparticle
friction coefficient.
article_number: '012301'
article_processing_charge: No
article_type: original
author:
- first_name: Tim
full_name: Still, Tim
last_name: Still
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Ke
full_name: Chen, Ke
last_name: Chen
- first_name: Peter J.
full_name: Yunker, Peter J.
last_name: Yunker
- first_name: Samuel
full_name: Schoenholz, Samuel
last_name: Schoenholz
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: A. G.
full_name: Yodh, A. G.
last_name: Yodh
citation:
ama: Still T, Goodrich CP, Chen K, et al. Phonon dispersion and elastic moduli of
two-dimensional disordered colloidal packings of soft particles with frictional
interactions. Physical Review E. 2014;89(1). doi:10.1103/physreve.89.012301
apa: Still, T., Goodrich, C. P., Chen, K., Yunker, P. J., Schoenholz, S., Liu, A.
J., & Yodh, A. G. (2014). Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions.
Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.012301
chicago: Still, Tim, Carl Peter Goodrich, Ke Chen, Peter J. Yunker, Samuel Schoenholz,
Andrea J. Liu, and A. G. Yodh. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.012301.
ieee: T. Still et al., “Phonon dispersion and elastic moduli of two-dimensional
disordered colloidal packings of soft particles with frictional interactions,”
Physical Review E, vol. 89, no. 1. American Physical Society, 2014.
ista: Still T, Goodrich CP, Chen K, Yunker PJ, Schoenholz S, Liu AJ, Yodh AG. 2014.
Phonon dispersion and elastic moduli of two-dimensional disordered colloidal packings
of soft particles with frictional interactions. Physical Review E. 89(1), 012301.
mla: Still, Tim, et al. “Phonon Dispersion and Elastic Moduli of Two-Dimensional
Disordered Colloidal Packings of Soft Particles with Frictional Interactions.”
Physical Review E, vol. 89, no. 1, 012301, American Physical Society, 2014,
doi:10.1103/physreve.89.012301.
short: T. Still, C.P. Goodrich, K. Chen, P.J. Yunker, S. Schoenholz, A.J. Liu, A.G.
Yodh, Physical Review E 89 (2014).
date_created: 2020-04-30T11:43:02Z
date_published: 2014-01-03T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '03'
doi: 10.1103/physreve.89.012301
extern: '1'
fulldoi: https://doi.org/10.1103/physreve.89.012301
intvolume: ' 89'
issue: '1'
language:
- iso: eng
month: '01'
oa_version: None
publication: Physical Review E
publication_identifier:
issn:
- 1539-3755
- 1550-2376
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
status: public
title: Phonon dispersion and elastic moduli of two-dimensional disordered colloidal
packings of soft particles with frictional interactions
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 89
year: '2014'
...
---
_id: '7773'
abstract:
- lang: eng
text: 'For more than a century, physicists have described real solids in terms of
perturbations about perfect crystalline order1. Such an approach takes us only
so far: a glass, another ubiquitous form of rigid matter, cannot be described
in any meaningful sense as a defected crystal2. Is there an opposite extreme to
a crystal—a solid with complete disorder—that forms an alternative starting point
for understanding real materials? Here, we argue that the solid comprising particles
with finite-ranged interactions at the jamming transition3,4,5 constitutes such
a limit. It has been shown that the physics associated with this transition can
be extended to interactions that are long ranged6. We demonstrate that jamming
physics is not restricted to amorphous systems, but dominates the behaviour of
solids with surprisingly high order. Just as the free-electron and tight-binding
models represent two idealized cases from which to understand electronic structure1,
we identify two extreme limits of mechanical behaviour. Thus, the physics of jamming
can be set side by side with the physics of crystals to provide an organizing
structure for understanding the mechanical properties of solids over the entire
spectrum of disorder.'
article_processing_charge: No
article_type: original
author:
- first_name: Carl Peter
full_name: Goodrich, Carl Peter
id: EB352CD2-F68A-11E9-89C5-A432E6697425
last_name: Goodrich
orcid: 0000-0002-1307-5074
- first_name: Andrea J.
full_name: Liu, Andrea J.
last_name: Liu
- first_name: Sidney R.
full_name: Nagel, Sidney R.
last_name: Nagel
citation:
ama: Goodrich CP, Liu AJ, Nagel SR. Solids between the mechanical extremes of order
and disorder. Nature Physics. 2014;10(8):578-581. doi:10.1038/nphys3006
apa: Goodrich, C. P., Liu, A. J., & Nagel, S. R. (2014). Solids between the
mechanical extremes of order and disorder. Nature Physics. Springer Nature.
https://doi.org/10.1038/nphys3006
chicago: Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Solids between
the Mechanical Extremes of Order and Disorder.” Nature Physics. Springer
Nature, 2014. https://doi.org/10.1038/nphys3006.
ieee: C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Solids between the mechanical
extremes of order and disorder,” Nature Physics, vol. 10, no. 8. Springer
Nature, pp. 578–581, 2014.
ista: Goodrich CP, Liu AJ, Nagel SR. 2014. Solids between the mechanical extremes
of order and disorder. Nature Physics. 10(8), 578–581.
mla: Goodrich, Carl Peter, et al. “Solids between the Mechanical Extremes of Order
and Disorder.” Nature Physics, vol. 10, no. 8, Springer Nature, 2014, pp.
578–81, doi:10.1038/nphys3006.
short: C.P. Goodrich, A.J. Liu, S.R. Nagel, Nature Physics 10 (2014) 578–581.
date_created: 2020-04-30T11:43:29Z
date_published: 2014-07-06T00:00:00Z
date_updated: 2021-01-12T08:15:26Z
day: '06'
doi: 10.1038/nphys3006
extern: '1'
fulldoi: https://doi.org/10.1038/nphys3006
intvolume: ' 10'
issue: '8'
language:
- iso: eng
month: '07'
oa_version: None
page: 578-581
publication: Nature Physics
publication_identifier:
issn:
- 1745-2473
- 1745-2481
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Solids between the mechanical extremes of order and disorder
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2014'
...
---
_id: '8021'
abstract:
- lang: eng
text: 'Most excitatory inputs in the mammalian brain are made on dendritic spines,
rather than on dendritic shafts. Spines compartmentalize calcium, and this biochemical
isolation can underlie input-specific synaptic plasticity, providing a raison
d''etre for spines. However, recent results indicate that the spine can experience
a membrane potential different from that in the parent dendrite, as though the
spine neck electrically isolated the spine. Here we use two-photon calcium imaging
of mouse neocortical pyramidal neurons to analyze the correlation between the
morphologies of spines activated under minimal synaptic stimulation and the excitatory
postsynaptic potentials they generate. We find that excitatory postsynaptic potential
amplitudes are inversely correlated with spine neck lengths. Furthermore, a spike
timing-dependent plasticity protocol, in which two-photon glutamate uncaging over
a spine is paired with postsynaptic spikes, produces rapid shrinkage of the spine
neck and concomitant increases in the amplitude of the evoked spine potentials.
Using numerical simulations, we explore the parameter regimes for the spine neck
resistance and synaptic conductance changes necessary to explain our observations.
Our data, directly correlating synaptic and morphological plasticity, imply that
long-necked spines have small or negligible somatic voltage contributions, but
that, upon synaptic stimulation paired with postsynaptic activity, they can shorten
their necks and increase synaptic efficacy, thus changing the input/output gain
of pyramidal neurons. '
article_processing_charge: No
article_type: original
author:
- first_name: R.
full_name: Araya, R.
last_name: Araya
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: R.
full_name: Yuste, R.
last_name: Yuste
citation:
ama: Araya R, Vogels TP, Yuste R. Activity-dependent dendritic spine neck changes
are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 2014;111(28):E2895-E2904. doi:10.1073/pnas.1321869111
apa: Araya, R., Vogels, T. P., & Yuste, R. (2014). Activity-dependent dendritic
spine neck changes are correlated with synaptic strength. Proceedings of the
National Academy of Sciences. Proceedings of the National Academy of Sciences.
https://doi.org/10.1073/pnas.1321869111
chicago: Araya, R., Tim P Vogels, and R. Yuste. “Activity-Dependent Dendritic Spine
Neck Changes Are Correlated with Synaptic Strength.” Proceedings of the National
Academy of Sciences. Proceedings of the National Academy of Sciences, 2014.
https://doi.org/10.1073/pnas.1321869111.
ieee: R. Araya, T. P. Vogels, and R. Yuste, “Activity-dependent dendritic spine
neck changes are correlated with synaptic strength,” Proceedings of the National
Academy of Sciences, vol. 111, no. 28. Proceedings of the National Academy
of Sciences, pp. E2895–E2904, 2014.
ista: Araya R, Vogels TP, Yuste R. 2014. Activity-dependent dendritic spine neck
changes are correlated with synaptic strength. Proceedings of the National Academy
of Sciences. 111(28), E2895–E2904.
mla: Araya, R., et al. “Activity-Dependent Dendritic Spine Neck Changes Are Correlated
with Synaptic Strength.” Proceedings of the National Academy of Sciences,
vol. 111, no. 28, Proceedings of the National Academy of Sciences, 2014, pp. E2895–904,
doi:10.1073/pnas.1321869111.
short: R. Araya, T.P. Vogels, R. Yuste, Proceedings of the National Academy of Sciences
111 (2014) E2895–E2904.
date_created: 2020-06-25T13:06:24Z
date_published: 2014-07-15T00:00:00Z
date_updated: 2021-01-12T08:16:34Z
day: '15'
doi: 10.1073/pnas.1321869111
extern: '1'
external_id:
pmid:
- '24982196'
fulldoi: https://doi.org/10.1073/pnas.1321869111
intvolume: ' 111'
issue: '28'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4104910/
month: '07'
oa: 1
oa_version: Published Version
page: E2895-E2904
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
status: public
title: Activity-dependent dendritic spine neck changes are correlated with synaptic
strength
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 111
year: '2014'
...
---
_id: '8022'
abstract:
- lang: eng
text: Populations of neurons in motor cortex engage in complex transient dynamics
of large amplitude during the execution of limb movements. Traditional network
models with stochastically assigned synapses cannot reproduce this behavior. Here
we introduce a class of cortical architectures with strong and random excitatory
recurrence that is stabilized by intricate, fine-tuned inhibition, optimized from
a control theory perspective. Such networks transiently amplify specific activity
states and can be used to reliably execute multidimensional movement patterns.
Similar to the experimental observations, these transients must be preceded by
a steady-state initialization phase from which the network relaxes back into the
background state by way of complex internal dynamics. In our networks, excitation
and inhibition are as tightly balanced as recently reported in experiments across
several brain areas, suggesting inhibitory control of complex excitatory recurrence
as a generic organizational principle in cortex.
article_processing_charge: No
article_type: original
author:
- first_name: Guillaume
full_name: Hennequin, Guillaume
last_name: Hennequin
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
citation:
ama: Hennequin G, Vogels TP, Gerstner W. Optimal control of transient dynamics in
balanced networks supports generation of complex movements. Neuron. 2014;82(6):1394-1406.
doi:10.1016/j.neuron.2014.04.045
apa: Hennequin, G., Vogels, T. P., & Gerstner, W. (2014). Optimal control of
transient dynamics in balanced networks supports generation of complex movements.
Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.045
chicago: Hennequin, Guillaume, Tim P Vogels, and Wulfram Gerstner. “Optimal Control
of Transient Dynamics in Balanced Networks Supports Generation of Complex Movements.”
Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.045.
ieee: G. Hennequin, T. P. Vogels, and W. Gerstner, “Optimal control of transient
dynamics in balanced networks supports generation of complex movements,” Neuron,
vol. 82, no. 6. Elsevier, pp. 1394–1406, 2014.
ista: Hennequin G, Vogels TP, Gerstner W. 2014. Optimal control of transient dynamics
in balanced networks supports generation of complex movements. Neuron. 82(6),
1394–1406.
mla: Hennequin, Guillaume, et al. “Optimal Control of Transient Dynamics in Balanced
Networks Supports Generation of Complex Movements.” Neuron, vol. 82, no.
6, Elsevier, 2014, pp. 1394–406, doi:10.1016/j.neuron.2014.04.045.
short: G. Hennequin, T.P. Vogels, W. Gerstner, Neuron 82 (2014) 1394–1406.
date_created: 2020-06-25T13:07:37Z
date_published: 2014-06-18T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '18'
doi: 10.1016/j.neuron.2014.04.045
extern: '1'
external_id:
pmid:
- '24945778'
fulldoi: https://doi.org/10.1016/j.neuron.2014.04.045
intvolume: ' 82'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364799/
month: '06'
oa: 1
oa_version: Submitted Version
page: 1394-1406
pmid: 1
publication: Neuron
publication_identifier:
issn:
- 0896-6273
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Optimal control of transient dynamics in balanced networks supports generation
of complex movements
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 82
year: '2014'
...
---
_id: '8023'
abstract:
- lang: eng
text: Uniform random sparse network architectures are ubiquitous in computational
neuroscience, but the implicit hypothesis that they are a good representation
of real neuronal networks has been met with skepticism. Here we used two experimental
data sets, a study of triplet connectivity statistics and a data set measuring
neuronal responses to channelrhodopsin stimuli, to evaluate the fidelity of thousands
of model networks. Network architectures comprised three neuron types (excitatory,
fast spiking, and nonfast spiking inhibitory) and were created from a set of rules
that govern the statistics of the resulting connection types. In a high-dimensional
parameter scan, we varied the degree distributions (i.e., how many cells each
neuron connects with) and the synaptic weight correlations of synapses from or
onto the same neuron. These variations converted initially uniform random and
homogeneously connected networks, in which every neuron sent and received equal
numbers of synapses with equal synaptic strength distributions, to highly heterogeneous
networks in which the number of synapses per neuron, as well as average synaptic
strength of synapses from or to a neuron were variable. By evaluating the impact
of each variable on the network structure and dynamics, and their similarity to
the experimental data, we could falsify the uniform random sparse connectivity
hypothesis for 7 of 36 connectivity parameters, but we also confirmed the hypothesis
in 8 cases. Twenty-one parameters had no substantial impact on the results of
the test protocols we used.
article_processing_charge: No
article_type: original
author:
- first_name: Christian
full_name: Tomm, Christian
last_name: Tomm
- first_name: Michael
full_name: Avermann, Michael
last_name: Avermann
- first_name: Carl
full_name: Petersen, Carl
last_name: Petersen
- first_name: Wulfram
full_name: Gerstner, Wulfram
last_name: Gerstner
- first_name: Tim P
full_name: Vogels, Tim P
id: CB6FF8D2-008F-11EA-8E08-2637E6697425
last_name: Vogels
orcid: 0000-0003-3295-6181
citation:
ama: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 2014;112(8):1801-1814. doi:10.1152/jn.00629.2013
apa: Tomm, C., Avermann, M., Petersen, C., Gerstner, W., & Vogels, T. P. (2014).
Connection-type-specific biases make uniform random network models consistent
with cortical recordings. Journal of Neurophysiology. American Physiological
Society. https://doi.org/10.1152/jn.00629.2013
chicago: Tomm, Christian, Michael Avermann, Carl Petersen, Wulfram Gerstner, and
Tim P Vogels. “Connection-Type-Specific Biases Make Uniform Random Network Models
Consistent with Cortical Recordings.” Journal of Neurophysiology. American
Physiological Society, 2014. https://doi.org/10.1152/jn.00629.2013.
ieee: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, and T. P. Vogels, “Connection-type-specific
biases make uniform random network models consistent with cortical recordings,”
Journal of Neurophysiology, vol. 112, no. 8. American Physiological Society,
pp. 1801–1814, 2014.
ista: Tomm C, Avermann M, Petersen C, Gerstner W, Vogels TP. 2014. Connection-type-specific
biases make uniform random network models consistent with cortical recordings.
Journal of Neurophysiology. 112(8), 1801–1814.
mla: Tomm, Christian, et al. “Connection-Type-Specific Biases Make Uniform Random
Network Models Consistent with Cortical Recordings.” Journal of Neurophysiology,
vol. 112, no. 8, American Physiological Society, 2014, pp. 1801–14, doi:10.1152/jn.00629.2013.
short: C. Tomm, M. Avermann, C. Petersen, W. Gerstner, T.P. Vogels, Journal of Neurophysiology
112 (2014) 1801–1814.
date_created: 2020-06-25T13:08:30Z
date_published: 2014-10-15T00:00:00Z
date_updated: 2021-01-12T08:16:35Z
day: '15'
ddc:
- '570'
doi: 10.1152/jn.00629.2013
extern: '1'
external_id:
pmid:
- '24944218'
file:
- access_level: open_access
checksum: 7c06a086da6f924342650de6dc555c3f
content_type: application/pdf
creator: cziletti
date_created: 2020-07-16T10:12:13Z
date_updated: 2020-07-16T10:12:13Z
file_id: '8122'
file_name: 2014_JNeurophysiol_Tomm.pdf
file_size: 1632295
relation: main_file
success: 1
file_date_updated: 2020-07-16T10:12:13Z
fulldoi: https://doi.org/10.1152/jn.00629.2013
has_accepted_license: '1'
intvolume: ' 112'
issue: '8'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
page: 1801-1814
pmid: 1
publication: Journal of Neurophysiology
publication_identifier:
eissn:
- 1522-1598
issn:
- 0022-3077
publication_status: published
publisher: American Physiological Society
quality_controlled: '1'
status: public
title: Connection-type-specific biases make uniform random network models consistent
with cortical recordings
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode
name: Creative Commons Attribution 3.0 Unported (CC BY 3.0)
short: CC BY (3.0)
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 112
year: '2014'
...
---
OA_place: publisher
OA_type: free access
_id: '8044'
abstract:
- lang: eng
text: Many questions concerning models in quantum mechanics require a detailed analysis
of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable
Hilbert space. Of particular relevance for an understanding of the low-temperature
properties of a system is the structure of the excitation spectrum, which is the
part of the spectrum close to the spectral bottom. We present recent progress
on this question for bosonic many-body quantum systems with weak two-body interactions.
Such system are currently of great interest, due to their experimental realization
in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations,
which predicts that the low-energy spectrum is made up of sums of elementary excitations,
with linear dispersion law at low momentum. The latter property is crucial for
the superfluid behavior the system.
article_processing_charge: No
author:
- first_name: Robert
full_name: Seiringer, Robert
id: 4AFD0470-F248-11E8-B48F-1D18A9856A87
last_name: Seiringer
orcid: 0000-0002-6781-0521
citation:
ama: 'Seiringer R. Structure of the excitation spectrum for many-body quantum systems.
In: Proceeding of the International Congress of Mathematicans. Vol 3. International
Congress of Mathematicians; 2014:1175-1194.'
apa: 'Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum
systems. In Proceeding of the International Congress of Mathematicans (Vol.
3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.'
chicago: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body
Quantum Systems.” In Proceeding of the International Congress of Mathematicans,
3:1175–94. International Congress of Mathematicians, 2014.
ieee: R. Seiringer, “Structure of the excitation spectrum for many-body quantum
systems,” in Proceeding of the International Congress of Mathematicans,
Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.
ista: 'Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum
systems. Proceeding of the International Congress of Mathematicans. ICM: International
Congress of Mathematicans vol. 3, 1175–1194.'
mla: Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum
Systems.” Proceeding of the International Congress of Mathematicans, vol.
3, International Congress of Mathematicians, 2014, pp. 1175–94.
short: R. Seiringer, in:, Proceeding of the International Congress of Mathematicans,
International Congress of Mathematicians, 2014, pp. 1175–1194.
conference:
end_date: 2014-08-21
location: Seoul, South Korea
name: 'ICM: International Congress of Mathematicans'
start_date: 2014-08-13
corr_author: '1'
date_created: 2020-06-29T07:59:35Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2026-06-18T19:30:06Z
day: '01'
ddc:
- '500'
department:
- _id: RoSe
intvolume: ' 3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://www.icm2014.org/en/vod/proceedings.html
month: '08'
oa: 1
oa_version: Published Version
page: 1175-1194
publication: Proceeding of the International Congress of Mathematicans
publication_identifier:
isbn:
- '9788961058063'
publication_status: published
publisher: International Congress of Mathematicians
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure of the excitation spectrum for many-body quantum systems
type: conference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 3
year: '2014'
...
---
_id: '8244'
abstract:
- lang: eng
text: Passive immunotherapy with monoclonal antibodies represents a cornerstone
of human anticancer therapies, but has not been established in veterinary medicine
yet. As the tumor-associated antigen EGFR (ErbB-1) is highly conserved between
humans and dogs, and considering the effectiveness of the anti-EGFR antibody cetuximab
in human clinical oncology, we present here a “caninized” version of this antibody,
can225IgG, for comparative oncology studies. Variable region genes of 225, the
murine precursor of cetuximab, were fused with canine constant heavy gamma and
kappa chain genes, respectively, and transfected into Chinese hamster ovary (CHO)
DUKX-B11 cells. Of note, 480 clones were screened and the best clones were selected
according to productivity and highest specificity in EGFR-coated ELISA. Upon purification
with Protein G, the recombinant cetuximab-like canine IgG was tested for integrity,
correct assembly, and functionality. Specific binding to the surface of EGFR-overexpressing
cells was assessed by flow cytometry and immunofluorescence; moreover, binding
to canine mammary tissue was demonstrated by immunohistochemistry. In cell viability
and proliferation assays, incubation with can225IgG led to significant tumor cell
growth inhibition. Moreover, this antibody mediated significant tumor cell killing
via phagocytosis in vitro. We thus present here, for the first time, the generation
of a canine IgG antibody and its hypothetical structure. On the basis of its cetuximab-like
binding site, on the one hand, and the expression of a 91% homologous EGFR molecule
in canine cancer, on the other hand, this antibody may be a promising research
compound to establish passive immunotherapy in dog patients with cancer.
article_processing_charge: No
article_type: original
author:
- first_name: J.
full_name: Singer, J.
last_name: Singer
- first_name: Judit
full_name: Fazekas, Judit
id: 36432834-F248-11E8-B48F-1D18A9856A87
last_name: Fazekas
orcid: 0000-0002-8777-3502
- first_name: W.
full_name: Wang, W.
last_name: Wang
- first_name: M.
full_name: Weichselbaumer, M.
last_name: Weichselbaumer
- first_name: M.
full_name: Matz, M.
last_name: Matz
- first_name: A.
full_name: Mader, A.
last_name: Mader
- first_name: W.
full_name: Steinfellner, W.
last_name: Steinfellner
- first_name: S.
full_name: Meitz, S.
last_name: Meitz
- first_name: D.
full_name: Mechtcheriakova, D.
last_name: Mechtcheriakova
- first_name: Y.
full_name: Sobanov, Y.
last_name: Sobanov
- first_name: M.
full_name: Willmann, M.
last_name: Willmann
- first_name: T.
full_name: Stockner, T.
last_name: Stockner
- first_name: E.
full_name: Spillner, E.
last_name: Spillner
- first_name: R.
full_name: Kunert, R.
last_name: Kunert
- first_name: E.
full_name: Jensen-Jarolim, E.
last_name: Jensen-Jarolim
citation:
ama: Singer J, Singer J, Wang W, et al. Generation of a canine anti-EGFR (ErbB-1)
antibody for passive immunotherapy in dog cancer patients. Molecular Cancer
Therapeutics. 2014;13(7):1777-1790. doi:10.1158/1535-7163.mct-13-0288
apa: Singer, J., Singer, J., Wang, W., Weichselbaumer, M., Matz, M., Mader, A.,
… Jensen-Jarolim, E. (2014). Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
American Association for Cancer Research. https://doi.org/10.1158/1535-7163.mct-13-0288
chicago: Singer, J., Judit Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader,
W. Steinfellner, et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics.
American Association for Cancer Research, 2014. https://doi.org/10.1158/1535-7163.mct-13-0288.
ieee: J. Singer et al., “Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients,” Molecular Cancer Therapeutics,
vol. 13, no. 7. American Association for Cancer Research, pp. 1777–1790, 2014.
ista: Singer J, Singer J, Wang W, Weichselbaumer M, Matz M, Mader A, Steinfellner
W, Meitz S, Mechtcheriakova D, Sobanov Y, Willmann M, Stockner T, Spillner E,
Kunert R, Jensen-Jarolim E. 2014. Generation of a canine anti-EGFR (ErbB-1) antibody
for passive immunotherapy in dog cancer patients. Molecular Cancer Therapeutics.
13(7), 1777–1790.
mla: Singer, J., et al. “Generation of a Canine Anti-EGFR (ErbB-1) Antibody for
Passive Immunotherapy in Dog Cancer Patients.” Molecular Cancer Therapeutics,
vol. 13, no. 7, American Association for Cancer Research, 2014, pp. 1777–90, doi:10.1158/1535-7163.mct-13-0288.
short: J. Singer, J. Singer, W. Wang, M. Weichselbaumer, M. Matz, A. Mader, W. Steinfellner,
S. Meitz, D. Mechtcheriakova, Y. Sobanov, M. Willmann, T. Stockner, E. Spillner,
R. Kunert, E. Jensen-Jarolim, Molecular Cancer Therapeutics 13 (2014) 1777–1790.
date_created: 2020-08-10T11:54:29Z
date_published: 2014-07-01T00:00:00Z
date_updated: 2021-01-12T08:17:42Z
day: '01'
doi: 10.1158/1535-7163.mct-13-0288
extern: '1'
fulldoi: https://doi.org/10.1158/1535-7163.mct-13-0288
intvolume: ' 13'
issue: '7'
language:
- iso: eng
month: '07'
oa_version: None
page: 1777-1790
publication: Molecular Cancer Therapeutics
publication_identifier:
issn:
- 1535-7163
- 1538-8514
publication_status: published
publisher: American Association for Cancer Research
quality_controlled: '1'
status: public
title: Generation of a canine anti-EGFR (ErbB-1) antibody for passive immunotherapy
in dog cancer patients
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 13
year: '2014'
...
---
_id: '8458'
abstract:
- lang: eng
text: The maintenance of bacterial cell shape and integrity is largely attributed
to peptidoglycan, a highly cross-linked biopolymer. The transpeptidases that perform
this cross-linking are important targets for antibiotics. Despite this biomedical
importance, to date no structure of a protein in complex with an intact bacterial
peptidoglycan has been resolved, primarily due to the large size and flexibility
of peptidoglycan sacculi. Here we use solid-state NMR spectroscopy to derive for
the first time an atomic model of an l,d-transpeptidase from Bacillus subtilis
bound to its natural substrate, the intact B. subtilis peptidoglycan. Importantly,
the model obtained from protein chemical shift perturbation data shows that both
domains—the catalytic domain as well as the proposed peptidoglycan recognition
domain—are important for the interaction and reveals a novel binding motif that
involves residues outside of the classical enzymatic pocket. Experiments on mutants
and truncated protein constructs independently confirm the binding site and the
implication of both domains. Through measurements of dipolar-coupling derived
order parameters of bond motion we show that protein binding reduces the flexibility
of peptidoglycan. This first report of an atomic model of a protein–peptidoglycan
complex paves the way for the design of new antibiotic drugs targeting l,d-transpeptidases.
The strategy developed here can be extended to the study of a large variety of
enzymes involved in peptidoglycan morphogenesis.
article_processing_charge: No
article_type: original
author:
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Sébastien
full_name: Triboulet, Sébastien
last_name: Triboulet
- first_name: Cédric
full_name: Laguri, Cédric
last_name: Laguri
- first_name: Catherine M.
full_name: Bougault, Catherine M.
last_name: Bougault
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Morgane
full_name: Callon, Morgane
last_name: Callon
- first_name: Michel
full_name: Arthur, Michel
last_name: Arthur
- first_name: Jean-Pierre
full_name: Simorre, Jean-Pierre
last_name: Simorre
citation:
ama: Schanda P, Triboulet S, Laguri C, et al. Atomic model of a cell-wall cross-linking
enzyme in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. 2014;136(51):17852-17860. doi:10.1021/ja5105987
apa: Schanda, P., Triboulet, S., Laguri, C., Bougault, C. M., Ayala, I., Callon,
M., … Simorre, J.-P. (2014). Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja5105987
chicago: Schanda, Paul, Sébastien Triboulet, Cédric Laguri, Catherine M. Bougault,
Isabel Ayala, Morgane Callon, Michel Arthur, and Jean-Pierre Simorre. “Atomic
Model of a Cell-Wall Cross-Linking Enzyme in Complex with an Intact Bacterial
Peptidoglycan.” Journal of the American Chemical Society. American Chemical
Society, 2014. https://doi.org/10.1021/ja5105987.
ieee: P. Schanda et al., “Atomic model of a cell-wall cross-linking enzyme
in complex with an intact bacterial peptidoglycan,” Journal of the American
Chemical Society, vol. 136, no. 51. American Chemical Society, pp. 17852–17860,
2014.
ista: Schanda P, Triboulet S, Laguri C, Bougault CM, Ayala I, Callon M, Arthur M,
Simorre J-P. 2014. Atomic model of a cell-wall cross-linking enzyme in complex
with an intact bacterial peptidoglycan. Journal of the American Chemical Society.
136(51), 17852–17860.
mla: Schanda, Paul, et al. “Atomic Model of a Cell-Wall Cross-Linking Enzyme in
Complex with an Intact Bacterial Peptidoglycan.” Journal of the American Chemical
Society, vol. 136, no. 51, American Chemical Society, 2014, pp. 17852–60,
doi:10.1021/ja5105987.
short: P. Schanda, S. Triboulet, C. Laguri, C.M. Bougault, I. Ayala, M. Callon,
M. Arthur, J.-P. Simorre, Journal of the American Chemical Society 136 (2014)
17852–17860.
date_created: 2020-09-18T10:07:52Z
date_published: 2014-11-27T00:00:00Z
date_updated: 2021-01-12T08:19:24Z
day: '27'
doi: 10.1021/ja5105987
extern: '1'
fulldoi: https://doi.org/10.1021/ja5105987
intvolume: ' 136'
issue: '51'
language:
- iso: eng
month: '11'
oa_version: None
page: 17852-17860
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Atomic model of a cell-wall cross-linking enzyme in complex with an intact
bacterial peptidoglycan
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 136
year: '2014'
...
---
_id: '8459'
abstract:
- lang: eng
text: Nuclear magnetic resonance (NMR) is a powerful tool for observing the motion
of biomolecules at the atomic level. One technique, the analysis of relaxation
dispersion phenomenon, is highly suited for studying the kinetics and thermodynamics
of biological processes. Built on top of the relax computational environment for
NMR dynamics is a new dispersion analysis designed to be comprehensive, accurate
and easy-to-use. The software supports more models, both numeric and analytic,
than current solutions. An automated protocol, available for scripting and driving
the graphical user interface (GUI), is designed to simplify the analysis of dispersion
data for NMR spectroscopists. Decreases in optimization time are granted by parallelization
for running on computer clusters and by skipping an initial grid search by using
parameters from one solution as the starting point for another —using analytic
model results for the numeric models, taking advantage of model nesting, and using
averaged non-clustered results for the clustered analysis.
article_processing_charge: No
article_type: original
author:
- first_name: Sébastien
full_name: Morin, Sébastien
last_name: Morin
- first_name: Troels E
full_name: Linnet, Troels E
last_name: Linnet
- first_name: Mathilde
full_name: Lescanne, Mathilde
last_name: Lescanne
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Gary S
full_name: Thompson, Gary S
last_name: Thompson
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Kaare
full_name: Teilum, Kaare
last_name: Teilum
- first_name: Stéphane
full_name: Gagné, Stéphane
last_name: Gagné
- first_name: Dominique
full_name: Marion, Dominique
last_name: Marion
- first_name: Christian
full_name: Griesinger, Christian
last_name: Griesinger
- first_name: Martin
full_name: Blackledge, Martin
last_name: Blackledge
- first_name: Edward J
full_name: d’Auvergne, Edward J
last_name: d’Auvergne
citation:
ama: 'Morin S, Linnet TE, Lescanne M, et al. Relax: The analysis of biomolecular
kinetics and thermodynamics using NMR relaxation dispersion data. Bioinformatics.
2014;30(15):2219-2220. doi:10.1093/bioinformatics/btu166'
apa: 'Morin, S., Linnet, T. E., Lescanne, M., Schanda, P., Thompson, G. S., Tollinger,
M., … d’Auvergne, E. J. (2014). Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data. Bioinformatics. Oxford
University Press. https://doi.org/10.1093/bioinformatics/btu166'
chicago: 'Morin, Sébastien, Troels E Linnet, Mathilde Lescanne, Paul Schanda, Gary
S Thompson, Martin Tollinger, Kaare Teilum, et al. “Relax: The Analysis of Biomolecular
Kinetics and Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics.
Oxford University Press, 2014. https://doi.org/10.1093/bioinformatics/btu166.'
ieee: 'S. Morin et al., “Relax: The analysis of biomolecular kinetics and
thermodynamics using NMR relaxation dispersion data,” Bioinformatics, vol.
30, no. 15. Oxford University Press, pp. 2219–2220, 2014.'
ista: 'Morin S, Linnet TE, Lescanne M, Schanda P, Thompson GS, Tollinger M, Teilum
K, Gagné S, Marion D, Griesinger C, Blackledge M, d’Auvergne EJ. 2014. Relax:
The analysis of biomolecular kinetics and thermodynamics using NMR relaxation
dispersion data. Bioinformatics. 30(15), 2219–2220.'
mla: 'Morin, Sébastien, et al. “Relax: The Analysis of Biomolecular Kinetics and
Thermodynamics Using NMR Relaxation Dispersion Data.” Bioinformatics, vol.
30, no. 15, Oxford University Press, 2014, pp. 2219–20, doi:10.1093/bioinformatics/btu166.'
short: S. Morin, T.E. Linnet, M. Lescanne, P. Schanda, G.S. Thompson, M. Tollinger,
K. Teilum, S. Gagné, D. Marion, C. Griesinger, M. Blackledge, E.J. d’Auvergne,
Bioinformatics 30 (2014) 2219–2220.
date_created: 2020-09-18T10:08:07Z
date_published: 2014-08-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/bioinformatics/btu166
extern: '1'
fulldoi: https://doi.org/10.1093/bioinformatics/btu166
intvolume: ' 30'
issue: '15'
keyword:
- Statistics and Probability
- Computational Theory and Mathematics
- Biochemistry
- Molecular Biology
- Computational Mathematics
- Computer Science Applications
language:
- iso: eng
month: '08'
oa_version: None
page: 2219-2220
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
- 1460-2059
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1093/bioinformatics/btz397
status: public
title: 'Relax: The analysis of biomolecular kinetics and thermodynamics using NMR
relaxation dispersion data'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 30
year: '2014'
...
---
_id: '8460'
abstract:
- lang: eng
text: The function of proteins depends on their ability to sample a variety of states
differing in structure and free energy. Deciphering how the various thermally
accessible conformations are connected, and understanding their structures and
relative energies is crucial in rationalizing protein function. Many biomolecular
reactions take place within microseconds to milliseconds, and this timescale is
therefore of central functional importance. Here we show that R1ρ relaxation dispersion
experiments in magic‐angle‐spinning solid‐state NMR spectroscopy make it possible
to investigate the thermodynamics and kinetics of such exchange process, and gain
insight into structural features of short‐lived states.
article_processing_charge: No
article_type: original
author:
- first_name: Peixiang
full_name: Ma, Peixiang
last_name: Ma
- first_name: Jens D.
full_name: Haller, Jens D.
last_name: Haller
- first_name: Jérémy
full_name: Zajakala, Jérémy
last_name: Zajakala
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Dieter
full_name: Willbold, Dieter
last_name: Willbold
- first_name: Jérôme
full_name: Boisbouvier, Jérôme
last_name: Boisbouvier
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Ma P, Haller JD, Zajakala J, et al. Probing transient conformational states
of proteins by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte
Chemie International Edition. 2014;53(17):4312-4317. doi:10.1002/anie.201311275
apa: Ma, P., Haller, J. D., Zajakala, J., Macek, P., Sivertsen, A. C., Willbold,
D., … Schanda, P. (2014). Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie
International Edition. Wiley. https://doi.org/10.1002/anie.201311275
chicago: Ma, Peixiang, Jens D. Haller, Jérémy Zajakala, Pavel Macek, Astrid C. Sivertsen,
Dieter Willbold, Jérôme Boisbouvier, and Paul Schanda. “Probing Transient Conformational
States of Proteins by Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.”
Angewandte Chemie International Edition. Wiley, 2014. https://doi.org/10.1002/anie.201311275.
ieee: P. Ma et al., “Probing transient conformational states of proteins
by solid-state R1ρ relaxation-dispersion NMR spectroscopy,” Angewandte Chemie
International Edition, vol. 53, no. 17. Wiley, pp. 4312–4317, 2014.
ista: Ma P, Haller JD, Zajakala J, Macek P, Sivertsen AC, Willbold D, Boisbouvier
J, Schanda P. 2014. Probing transient conformational states of proteins by solid-state
R1ρ relaxation-dispersion NMR spectroscopy. Angewandte Chemie International Edition.
53(17), 4312–4317.
mla: Ma, Peixiang, et al. “Probing Transient Conformational States of Proteins by
Solid-State R1ρ Relaxation-Dispersion NMR Spectroscopy.” Angewandte Chemie
International Edition, vol. 53, no. 17, Wiley, 2014, pp. 4312–17, doi:10.1002/anie.201311275.
short: P. Ma, J.D. Haller, J. Zajakala, P. Macek, A.C. Sivertsen, D. Willbold, J.
Boisbouvier, P. Schanda, Angewandte Chemie International Edition 53 (2014) 4312–4317.
date_created: 2020-09-18T10:08:53Z
date_published: 2014-03-18T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '18'
doi: 10.1002/anie.201311275
extern: '1'
fulldoi: https://doi.org/10.1002/anie.201311275
intvolume: ' 53'
issue: '17'
language:
- iso: eng
month: '03'
oa_version: None
page: 4312-4317
publication: Angewandte Chemie International Edition
publication_identifier:
issn:
- 1433-7851
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Probing transient conformational states of proteins by solid-state R1ρ relaxation-dispersion
NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 53
year: '2014'
...
---
_id: '8500'
abstract:
- lang: eng
text: The main model studied in this paper is a lattice of pendula with a nearest‐neighbor
coupling. If the coupling is weak, then the system is near‐integrable and KAM
tori fill most of the phase space. For all KAM trajectories the energy of each
pendulum stays within a narrow band for all time. Still, we show that for an arbitrarily
weak coupling of a certain localized type, the neighboring pendula can exchange
energy. In fact, the energy can be transferred between the pendula in any prescribed
way.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Mark
full_name: Levi, Mark
last_name: Levi
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Levi M, Saprykina M. Arnol′d diffusion in a pendulum lattice. Communications
on Pure and Applied Mathematics. 2014;67(5):748-775. doi:10.1002/cpa.21509
apa: Kaloshin, V., Levi, M., & Saprykina, M. (2014). Arnol′d diffusion in a
pendulum lattice. Communications on Pure and Applied Mathematics. Wiley.
https://doi.org/10.1002/cpa.21509
chicago: Kaloshin, Vadim, Mark Levi, and Maria Saprykina. “Arnol′d Diffusion in
a Pendulum Lattice.” Communications on Pure and Applied Mathematics. Wiley,
2014. https://doi.org/10.1002/cpa.21509.
ieee: V. Kaloshin, M. Levi, and M. Saprykina, “Arnol′d diffusion in a pendulum lattice,”
Communications on Pure and Applied Mathematics, vol. 67, no. 5. Wiley,
pp. 748–775, 2014.
ista: Kaloshin V, Levi M, Saprykina M. 2014. Arnol′d diffusion in a pendulum lattice.
Communications on Pure and Applied Mathematics. 67(5), 748–775.
mla: Kaloshin, Vadim, et al. “Arnol′d Diffusion in a Pendulum Lattice.” Communications
on Pure and Applied Mathematics, vol. 67, no. 5, Wiley, 2014, pp. 748–75,
doi:10.1002/cpa.21509.
short: V. Kaloshin, M. Levi, M. Saprykina, Communications on Pure and Applied Mathematics
67 (2014) 748–775.
date_created: 2020-09-18T10:47:01Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2022-08-25T13:58:13Z
day: '01'
doi: 10.1002/cpa.21509
extern: '1'
fulldoi: https://doi.org/10.1002/cpa.21509
intvolume: ' 67'
issue: '5'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '05'
oa_version: None
page: 748-775
publication: Communications on Pure and Applied Mathematics
publication_identifier:
issn:
- 0010-3640
publication_status: published
publisher: Wiley
quality_controlled: '1'
status: public
title: Arnol′d diffusion in a pendulum lattice
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 67
year: '2014'
...
---
_id: '8501'
abstract:
- lang: eng
text: In this paper, we study small perturbations of a class of non-convex integrable
Hamiltonians with two degrees of freedom, and we prove a result of diffusion for
an open and dense set of perturbations, with an optimal time of diffusion which
grows linearly with respect to the inverse of the size of the perturbation.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Abed
full_name: Bounemoura, Abed
last_name: Bounemoura
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Bounemoura A, Kaloshin V. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal.
2014;14(2):181-203. doi:10.17323/1609-4514-2014-14-2-181-203
apa: Bounemoura, A., & Kaloshin, V. (2014). Generic fast diffusion for a class
of non-convex Hamiltonians with two degrees of freedom. Moscow Mathematical
Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-2-181-203
chicago: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class
of Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical
Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-2-181-203.
ieee: A. Bounemoura and V. Kaloshin, “Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom,” Moscow Mathematical Journal,
vol. 14, no. 2. Independent University of Moscow, pp. 181–203, 2014.
ista: Bounemoura A, Kaloshin V. 2014. Generic fast diffusion for a class of non-convex
Hamiltonians with two degrees of freedom. Moscow Mathematical Journal. 14(2),
181–203.
mla: Bounemoura, Abed, and Vadim Kaloshin. “Generic Fast Diffusion for a Class of
Non-Convex Hamiltonians with Two Degrees of Freedom.” Moscow Mathematical Journal,
vol. 14, no. 2, Independent University of Moscow, 2014, pp. 181–203, doi:10.17323/1609-4514-2014-14-2-181-203.
short: A. Bounemoura, V. Kaloshin, Moscow Mathematical Journal 14 (2014) 181–203.
date_created: 2020-09-18T10:47:09Z
date_published: 2014-04-01T00:00:00Z
date_updated: 2021-01-12T08:19:43Z
day: '01'
doi: 10.17323/1609-4514-2014-14-2-181-203
extern: '1'
external_id:
arxiv:
- '1304.3050'
fulldoi: https://doi.org/10.17323/1609-4514-2014-14-2-181-203
intvolume: ' 14'
issue: '2'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: Preprint
page: 181-203
publication: Moscow Mathematical Journal
publication_identifier:
issn:
- 1609-3321
- 1609-4514
publication_status: published
publisher: Independent University of Moscow
quality_controlled: '1'
status: public
title: Generic fast diffusion for a class of non-convex Hamiltonians with two degrees
of freedom
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 14
year: '2014'
...
---
_id: '9050'
abstract:
- lang: eng
text: Self-propelled particles can exhibit surprising non-equilibrium behaviors,
and how they interact with obstacles or boundaries remains an important open problem.
Here we show that chemically propelled micro-rods can be captured, with little
change in their speed, into close orbits around solid spheres resting on or near
a horizontal plane. We show that this interaction between sphere and particle
is short-range, occurring even for spheres smaller than the particle length, and
for a variety of sphere materials. We consider a simple model, based on lubrication
theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic
propulsion mechanism) and moving near a solid surface. The model demonstrates
capture, or movement towards the surface, and yields speeds independent of distance.
This study reveals the crucial aspects of activity–driven interactions of self-propelled
particles with passive objects, and brings into question the use of colloidal
tracers as probes of active matter.
article_number: '1784'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Daisuke
full_name: Takagi, Daisuke
last_name: Takagi
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: Adam B.
full_name: Braunschweig, Adam B.
last_name: Braunschweig
- first_name: Michael J.
full_name: Shelley, Michael J.
last_name: Shelley
- first_name: Jun
full_name: Zhang, Jun
last_name: Zhang
citation:
ama: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. Hydrodynamic capture
of microswimmers into sphere-bound orbits. Soft Matter. 2014;10(11). doi:10.1039/c3sm52815d
apa: Takagi, D., Palacci, J. A., Braunschweig, A. B., Shelley, M. J., & Zhang,
J. (2014). Hydrodynamic capture of microswimmers into sphere-bound orbits. Soft
Matter. Royal Society of Chemistry . https://doi.org/10.1039/c3sm52815d
chicago: Takagi, Daisuke, Jérémie A Palacci, Adam B. Braunschweig, Michael J. Shelley,
and Jun Zhang. “Hydrodynamic Capture of Microswimmers into Sphere-Bound Orbits.”
Soft Matter. Royal Society of Chemistry , 2014. https://doi.org/10.1039/c3sm52815d.
ieee: D. Takagi, J. A. Palacci, A. B. Braunschweig, M. J. Shelley, and J. Zhang,
“Hydrodynamic capture of microswimmers into sphere-bound orbits,” Soft Matter,
vol. 10, no. 11. Royal Society of Chemistry , 2014.
ista: Takagi D, Palacci JA, Braunschweig AB, Shelley MJ, Zhang J. 2014. Hydrodynamic
capture of microswimmers into sphere-bound orbits. Soft Matter. 10(11), 1784.
mla: Takagi, Daisuke, et al. “Hydrodynamic Capture of Microswimmers into Sphere-Bound
Orbits.” Soft Matter, vol. 10, no. 11, 1784, Royal Society of Chemistry
, 2014, doi:10.1039/c3sm52815d.
short: D. Takagi, J.A. Palacci, A.B. Braunschweig, M.J. Shelley, J. Zhang, Soft
Matter 10 (2014).
date_created: 2021-02-01T13:43:31Z
date_published: 2014-03-21T00:00:00Z
date_updated: 2023-02-23T13:47:35Z
day: '21'
doi: 10.1039/c3sm52815d
extern: '1'
external_id:
arxiv:
- '1309.5662'
pmid:
- '24800268'
fulldoi: https://doi.org/10.1039/c3sm52815d
intvolume: ' 10'
issue: '11'
keyword:
- General Chemistry
- Condensed Matter Physics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1309.5662
month: '03'
oa: 1
oa_version: Preprint
pmid: 1
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: 'Royal Society of Chemistry '
quality_controlled: '1'
scopus_import: '1'
status: public
title: Hydrodynamic capture of microswimmers into sphere-bound orbits
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2014'
...
---
_id: '9166'
abstract:
- lang: eng
text: Light-activated self-propelled colloids are synthesized and their active motion
is studied using optical microscopy. We propose a versatile route using different
photoactive materials, and demonstrate a multiwavelength activation and propulsion.
Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3
and TiO2), a light with an energy higher than the bandgap triggers the reaction
of decomposition of hydrogen peroxide and produces a chemical cloud around the
particle. It induces a phoretic attraction with neighbouring colloids as well
as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms
to form colloidal cargos as well as self-propelled particles where the light-activated
component is embedded into a dielectric sphere. The particles are self-propelled
along a direction otherwise randomized by thermal fluctuations, and exhibit a
persistent random walk. For sufficient surface density, the particles spontaneously
form ‘living crystals’ which are mobile, break apart and reform. Steering the
particle with an external magnetic field, we show that the formation of the dense
phase results from the collisions heads-on of the particles. This effect is intrinsically
non-equilibrium and a novel principle of organization for systems without detailed
balance. Engineering families of particles self-propelled by different wavelength
demonstrate a good understanding of both the physics and the chemistry behind
the system and points to a general route for designing new families of self-propelled
particles.
article_number: '20130372'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
- first_name: S.
full_name: Sacanna, S.
last_name: Sacanna
- first_name: S.-H.
full_name: Kim, S.-H.
last_name: Kim
- first_name: G.-R.
full_name: Yi, G.-R.
last_name: Yi
- first_name: D. J.
full_name: Pine, D. J.
last_name: Pine
- first_name: P. M.
full_name: Chaikin, P. M.
last_name: Chaikin
citation:
ama: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A:
Mathematical, Physical and Engineering Sciences. 2014;372(2029). doi:10.1098/rsta.2013.0372'
apa: 'Palacci, J. A., Sacanna, S., Kim, S.-H., Yi, G.-R., Pine, D. J., & Chaikin,
P. M. (2014). Light-activated self-propelled colloids. Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society. https://doi.org/10.1098/rsta.2013.0372'
chicago: 'Palacci, Jérémie A, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P.
M. Chaikin. “Light-Activated Self-Propelled Colloids.” Philosophical Transactions
of the Royal Society A: Mathematical, Physical and Engineering Sciences. The
Royal Society, 2014. https://doi.org/10.1098/rsta.2013.0372.'
ieee: 'J. A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D. J. Pine, and P. M. Chaikin,
“Light-activated self-propelled colloids,” Philosophical Transactions of the
Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 372,
no. 2029. The Royal Society, 2014.'
ista: 'Palacci JA, Sacanna S, Kim S-H, Yi G-R, Pine DJ, Chaikin PM. 2014. Light-activated
self-propelled colloids. Philosophical Transactions of the Royal Society A: Mathematical,
Physical and Engineering Sciences. 372(2029), 20130372.'
mla: 'Palacci, Jérémie A., et al. “Light-Activated Self-Propelled Colloids.” Philosophical
Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences,
vol. 372, no. 2029, 20130372, The Royal Society, 2014, doi:10.1098/rsta.2013.0372.'
short: 'J.A. Palacci, S. Sacanna, S.-H. Kim, G.-R. Yi, D.J. Pine, P.M. Chaikin,
Philosophical Transactions of the Royal Society A: Mathematical, Physical and
Engineering Sciences 372 (2014).'
date_created: 2021-02-18T14:31:11Z
date_published: 2014-11-28T00:00:00Z
date_updated: 2021-02-22T10:44:16Z
day: '28'
doi: 10.1098/rsta.2013.0372
extern: '1'
external_id:
arxiv:
- '1410.7278'
pmid:
- '25332383'
fulldoi: https://doi.org/10.1098/rsta.2013.0372
intvolume: ' 372'
issue: '2029'
keyword:
- General Engineering
- General Physics and Astronomy
- General Mathematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1098/rsta.2013.0372
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: 'Philosophical Transactions of the Royal Society A: Mathematical, Physical
and Engineering Sciences'
publication_identifier:
eissn:
- 1471-2962
issn:
- 1364-503X
publication_status: published
publisher: The Royal Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Light-activated self-propelled colloids
type: journal_article
user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 372
year: '2014'
...
---
_id: '9458'
abstract:
- lang: eng
text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.
Their genomes are typically depleted of CG dinucleotides because of imperfect
repair of deaminated methylcytosines. Here, we extensively survey diverse species
lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless
frequently present and catalyzed by a different DNA methyltransferase family,
Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years
ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered
methylation occurs at unprecedented densities and directly disfavors nucleosomes,
contributing to nucleosome positioning between clusters. Dense methylation is
enabled by a regime of genomic sequence evolution that enriches CG dinucleotides
and drives the highest CG frequencies known. Species with linker methylation have
small, transcriptionally active nuclei that approach the physical limits of chromatin
compaction. These features constitute a previously unappreciated genome architecture,
in which dense methylation influences nucleosome positions, likely facilitating
nuclear processes under extreme spatial constraints.
article_processing_charge: No
article_type: original
author:
- first_name: Jason T.
full_name: Huff, Jason T.
last_name: Huff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome
positioning in diverse eukaryotes. Cell. 2014;156(6):1286-1297. doi:10.1016/j.cell.2014.01.029
apa: Huff, J. T., & Zilberman, D. (2014). Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.01.029
chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation
Contributes to Nucleosome Positioning in Diverse Eukaryotes.” Cell. Elsevier,
2014. https://doi.org/10.1016/j.cell.2014.01.029.
ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes
to nucleosome positioning in diverse eukaryotes,” Cell, vol. 156, no. 6.
Elsevier, pp. 1286–1297, 2014.
ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to
nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.
mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes
to Nucleosome Positioning in Diverse Eukaryotes.” Cell, vol. 156, no. 6,
Elsevier, 2014, pp. 1286–97, doi:10.1016/j.cell.2014.01.029.
short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
date_created: 2021-06-04T12:00:16Z
date_published: 2014-03-13T00:00:00Z
date_updated: 2021-12-14T08:22:36Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cell.2014.01.029
extern: '1'
external_id:
pmid:
- '24630728'
fulldoi: https://doi.org/10.1016/j.cell.2014.01.029
intvolume: ' 156'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cell.2014.01.029
month: '03'
oa: 1
oa_version: Published Version
page: 1286-1297
pmid: 1
publication: Cell
publication_identifier:
eissn:
- 1097-4172
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse
eukaryotes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 156
year: '2014'
...
---
_id: '9479'
abstract:
- lang: eng
text: Centromeres mediate chromosome segregation and are defined by the centromere-specific
histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from
centromeres is a general property of terminally differentiated cells, and the
persistence of CenH3 increases the risk of diseases such as cancer. However, active
mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen
vegetative cells, which transport engulfed sperm by extended tip growth, undergo
loss of CenH3; centromeric heterochromatin decondensation; and bulk activation
of silent rRNA genes, accompanied by their translocation into the nucleolus. Here,
we show that these processes are blocked by mutations in the evolutionarily conserved
AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97
proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier
(SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates
with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as
well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations.
In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are
uniquely clustered together within the nucleolus and all major rRNA gene variants,
including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant
vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed
centromeric heterochromatin at the external periphery of the nucleolus. Our results
indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres
and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus
for ribosome production, which fuels single nucleus-driven pollen tube growth
and is essential for plant reproduction.
article_processing_charge: No
article_type: original
author:
- first_name: Zsuzsanna
full_name: Mérai, Zsuzsanna
last_name: Mérai
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Marcelina
full_name: García-Aguilar, Marcelina
last_name: García-Aguilar
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: János
full_name: Bindics, János
last_name: Bindics
- first_name: Lucyna
full_name: Ślusarz, Lucyna
last_name: Ślusarz
- first_name: Stéphanie
full_name: Arnoux, Stéphanie
last_name: Arnoux
- first_name: Susanne
full_name: Opravil, Susanne
last_name: Opravil
- first_name: Karl
full_name: Mechtler, Karl
last_name: Mechtler
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
citation:
ama: Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone
Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and
activates ribosomal RNA genes. Proceedings of the National Academy of Sciences.
2014;111(45):16166-16171. doi:10.1073/pnas.1418564111
apa: Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft,
V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1418564111
chicago: Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh,
Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular
Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin,
and Activates Ribosomal RNA Genes.” Proceedings of the National Academy of
Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1418564111.
ieee: Z. Mérai et al., “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles
sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA
genes,” Proceedings of the National Academy of Sciences, vol. 111, no.
45. National Academy of Sciences, pp. 16166–16171, 2014.
ista: Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics
J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru
H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated
centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings
of the National Academy of Sciences. 111(45), 16166–16171.
mla: Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles
Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA
Genes.” Proceedings of the National Academy of Sciences, vol. 111, no.
45, National Academy of Sciences, 2014, pp. 16166–71, doi:10.1073/pnas.1418564111.
short: Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft,
J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L.
Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014)
16166–16171.
date_created: 2021-06-07T07:23:43Z
date_published: 2014-11-11T00:00:00Z
date_updated: 2021-12-14T08:23:26Z
day: '11'
department:
- _id: DaZi
doi: 10.1073/pnas.1418564111
extern: '1'
external_id:
pmid:
- '25344531'
fulldoi: https://doi.org/10.1073/pnas.1418564111
intvolume: ' 111'
issue: '45'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1418564111
month: '11'
oa: 1
oa_version: Published Version
page: 16166-16171
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres,
decondenses heterochromatin, and activates ribosomal RNA genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 111
year: '2014'
...
---
_id: '9519'
abstract:
- lang: eng
text: Transposons are selfish genetic sequences that can increase their copy number
and inflict substantial damage on their hosts. To combat these genomic parasites,
plants have evolved multiple pathways to identify and silence transposons by methylating
their DNA. Plants have also evolved mechanisms to limit the collateral damage
from the antitransposon machinery. In this review, we examine recent developments
that have elucidated many of the molecular workings of these pathways. We also
highlight the evidence that the methylation and demethylation pathways interact,
indicating that plants have a highly sophisticated, integrated system of transposon
defense that has an important role in the regulation of gene expression.
article_processing_charge: No
article_type: review
author:
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 2014;19(5):320-326. doi:10.1016/j.tplants.2014.01.014
apa: Kim, M. Y., & Zilberman, D. (2014). DNA methylation as a system of plant
genomic immunity. Trends in Plant Science. Elsevier. https://doi.org/10.1016/j.tplants.2014.01.014
chicago: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science. Elsevier, 2014. https://doi.org/10.1016/j.tplants.2014.01.014.
ieee: M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic
immunity,” Trends in Plant Science, vol. 19, no. 5. Elsevier, pp. 320–326,
2014.
ista: Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity.
Trends in Plant Science. 19(5), 320–326.
mla: Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant
Genomic Immunity.” Trends in Plant Science, vol. 19, no. 5, Elsevier, 2014,
pp. 320–26, doi:10.1016/j.tplants.2014.01.014.
short: M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.
date_created: 2021-06-07T14:38:09Z
date_published: 2014-05-04T00:00:00Z
date_updated: 2021-12-14T08:24:48Z
day: '04'
department:
- _id: DaZi
doi: 10.1016/j.tplants.2014.01.014
extern: '1'
external_id:
pmid:
- '24618094 '
fulldoi: https://doi.org/10.1016/j.tplants.2014.01.014
intvolume: ' 19'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 320-326
pmid: 1
publication: Trends in Plant Science
publication_identifier:
eissn:
- 1878-4372
issn:
- 1360-1385
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation as a system of plant genomic immunity
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 19
year: '2014'
...
---
_id: '9594'
abstract:
- lang: eng
text: Let d≥3 be a fixed integer. We give an asympotic formula for the expected
number of spanning trees in a uniformly random d-regular graph with n vertices.
(The asymptotics are as n→∞, restricted to even n if d is odd.) We also obtain
the asymptotic distribution of the number of spanning trees in a uniformly random
cubic graph, and conjecture that the corresponding result holds for arbitrary
(fixed) d. Numerical evidence is presented which supports our conjecture.
article_number: P1.45
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Catherine
full_name: Greenhill, Catherine
last_name: Greenhill
- first_name: Matthew Alan
full_name: Kwan, Matthew Alan
id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3
last_name: Kwan
orcid: 0000-0002-4003-7567
- first_name: David
full_name: Wind, David
last_name: Wind
citation:
ama: Greenhill C, Kwan MA, Wind D. On the number of spanning trees in random regular
graphs. The Electronic Journal of Combinatorics. 2014;21(1). doi:10.37236/3752
apa: Greenhill, C., Kwan, M. A., & Wind, D. (2014). On the number of spanning
trees in random regular graphs. The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics. https://doi.org/10.37236/3752
chicago: Greenhill, Catherine, Matthew Alan Kwan, and David Wind. “On the Number
of Spanning Trees in Random Regular Graphs.” The Electronic Journal of Combinatorics.
The Electronic Journal of Combinatorics, 2014. https://doi.org/10.37236/3752.
ieee: C. Greenhill, M. A. Kwan, and D. Wind, “On the number of spanning trees in
random regular graphs,” The Electronic Journal of Combinatorics, vol. 21,
no. 1. The Electronic Journal of Combinatorics, 2014.
ista: Greenhill C, Kwan MA, Wind D. 2014. On the number of spanning trees in random
regular graphs. The Electronic Journal of Combinatorics. 21(1), P1.45.
mla: Greenhill, Catherine, et al. “On the Number of Spanning Trees in Random Regular
Graphs.” The Electronic Journal of Combinatorics, vol. 21, no. 1, P1.45,
The Electronic Journal of Combinatorics, 2014, doi:10.37236/3752.
short: C. Greenhill, M.A. Kwan, D. Wind, The Electronic Journal of Combinatorics
21 (2014).
date_created: 2021-06-23T06:29:35Z
date_published: 2014-02-28T00:00:00Z
date_updated: 2023-02-23T14:02:12Z
day: '28'
doi: 10.37236/3752
extern: '1'
external_id:
arxiv:
- '1309.6710'
fulldoi: https://doi.org/10.37236/3752
intvolume: ' 21'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.37236/3752
month: '02'
oa: 1
oa_version: Published Version
publication: The Electronic Journal of Combinatorics
publication_identifier:
eissn:
- 1077-8926
publication_status: published
publisher: The Electronic Journal of Combinatorics
quality_controlled: '1'
scopus_import: '1'
status: public
title: On the number of spanning trees in random regular graphs
type: journal_article
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
volume: 21
year: '2014'
...